All Stories

  1. A finely balanced order–disorder equilibrium sculpts the folding–binding landscape of an antibiotic sequestering protein

    Article • Proceedings of the National Academy of Sciences, May 2024, Proceedings of the National Academy of Sciences

    Dr Athi N Naganathan, Marco D'Abramo

  2. A Theoretical‐Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature

    Article • ChemPhysChem, March 2024, Wiley

    Marco D'Abramo

  3. Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution

    Article • Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, February 2024, Elsevier

    Marco D'Abramo

  4. Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical–Computational Study

    Article • The Journal of Physical Chemistry B, October 2023, American Chemical Society (ACS)

    Marco D'Abramo

  5. ERAP1 and ERAP2 Haplotypes Influence Suboptimal HLA-B*27:05-Restricted Anti-Viral CD8+ T Cell Responses Cross-Reactive to Self-Epitopes

    Article • International Journal of Molecular Sciences, August 2023, MDPI AG

    Marco D'Abramo

  6. Unveiling the Excited State Dynamics of Indole in Solution

    Article • Journal of Chemical Theory and Computation, June 2023, American Chemical Society (ACS)

    Marco D'Abramo

  7. Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis

    Article • Molecules, February 2023, MDPI AG

    Marco D'Abramo

  8. Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP

    Article • Molecules, January 2023, MDPI AG

    Marco D'Abramo

  9. A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole

    Article • Molecules, November 2022, MDPI AG

    Marco D'Abramo

  10. Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense

    Article • International Journal of Molecular Sciences, November 2022, MDPI AG

    Marco D'Abramo

  11. PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method

    Article • Journal of Chemical Theory and Computation, November 2022, American Chemical Society (ACS)

    Marco D'Abramo

  12. Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases

    Article • Molecules, November 2022, MDPI AG

    Marco D'Abramo

  13. Effects of Environmental and Electric Perturbations on the pKa of Thioredoxin Cysteine 35: A Computational Study

    Article • Molecules, September 2022, MDPI AG

    Marco D'Abramo

  14. Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs

    Article • Journal of Chemical Information and Modeling, August 2022, American Chemical Society (ACS)

    Marco D'Abramo

  15. Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations

    Article • The Journal of Physical Chemistry B, June 2022, American Chemical Society (ACS)

    Marco D'Abramo

  16. Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein

    Article • ACS Omega, April 2022, American Chemical Society (ACS)

    Marco D'Abramo

  17. The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States

    Article • Cells, February 2022, MDPI AG

    Marco D'Abramo

  18. Theoretical Modeling of Redox Potentials of Biomolecules

    Article • Molecules, February 2022, MDPI AG

    Marco D'Abramo

  19. Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study

    Article • Physical Chemistry Chemical Physics, January 2022, Royal Society of Chemistry

    Marco D'Abramo

  20. Complexation and organization of doxorubicin on polystyrene sulfonate chains: impacts on doxorubicin dimerization and quenching

    Article • Physical Chemistry Chemical Physics, January 2022, Royal Society of Chemistry

    Marco D'Abramo

  21. Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics

    Article • Biomolecules, December 2021, MDPI AG

    Marco D'Abramo

  22. Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States

    Article • Journal of Chemical Information and Modeling, August 2021, American Chemical Society (ACS)

    Marco D'Abramo

  23. Modelling the Activation Pathways in Full-Length Src Kinase

    Article • Biophysica, June 2021, MDPI AG

    Marco D'Abramo

  24. Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution

    Article • Journal of Chemical Theory and Computation, February 2021, American Chemical Society (ACS)

    Marco D'Abramo

  25. Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches

    Article • Biomedicines, December 2020, MDPI AG

    Marco D'Abramo

  26. The full model of the pMHC-TCR-CD3 complex: a structural and kinetics characterization

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Marco D'Abramo

  27. Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions

    Article • Cells, April 2020, MDPI AG

    Marco D'Abramo

  28. Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors

    Article • Journal of Chemical Information and Modeling, February 2020, American Chemical Society (ACS)

    Marco D'Abramo

  29. EBV, CD8 and Ankylosing spondylitis

    Article • Cells, June 2019, MDPI AG

    Marco D'Abramo, Professor Rosa Sorrentino

  30. Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins

    Article • Journal of Molecular Evolution, May 2019, Springer Science + Business Media

    Marco D'Abramo

  31. On the activation and deactivation pathways of the Lck kinase domain: a computational study

    Article • Journal of Computer-Aided Molecular Design, May 2019, Springer Science + Business Media

    Marco D'Abramo

  32. Theoretical–computational modelling of the temperature dependence of the folding–unfolding thermodynamics and kinetics: the case of a Trp-cage

    Article • Physical Chemistry Chemical Physics, January 2019, Royal Society of Chemistry

    Marco D'Abramo

  33. Efficient and Accurate Modeling of Conformational Transitions in Proteins: The Case of c-Src Kinase

    Article • The Journal of Physical Chemistry B, September 2018, American Chemical Society (ACS)

    Marco D'Abramo

  34. Understanding the indirect DNA read-out specificity of I-CreI Meganuclease

    Article • Scientific Reports, July 2018, Springer Science + Business Media

    Marco D'Abramo

  35. A Stereochemically Driven Supramolecular Polymerisation

    Article • Chemistry - A European Journal, May 2018, Wiley

    Marco D'Abramo

  36. 2-(Hydroxyimino)aldehydes: Photo- and Physicochemical Properties of a Versatile Functional Group for Monomer Design

    Article • Chemistry - A European Journal, May 2018, Wiley

    Marco D'Abramo

  37. Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives

    Article • Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, April 2018, Elsevier

    Marco D'Abramo

  38. Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

    Article • Journal of Computer-Aided Molecular Design, November 2017, Springer Science + Business Media

    Marco D'Abramo

  39. Density discriminates between thermophilic and mesophilic proteins

    Article • Journal of Biomolecular Structure and Dynamics, October 2017, Taylor & Francis

    Marco D'Abramo

  40. Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

    Article • Biopolymers, September 2016, Wiley

    Marco D'Abramo

  41. Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II)

    Article • The Journal of Physical Chemistry A, May 2016, American Chemical Society (ACS)

    Marco D'Abramo

  42. Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment

    Article • Theoretical Chemistry Accounts, April 2016, Springer Science + Business Media

    Marco D'Abramo

  43. Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives

    Article • Colloids and Surfaces B Biointerfaces, April 2016, Elsevier

    Marco D'Abramo

  44. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics

    Article • ACS Chemical Biology, March 2016, American Chemical Society (ACS)

    Marco D'Abramo

  45. Role of the hydrophilic spacer of glucosylated amphiphiles included in liposome formulations in the recognition of Concanavalin A

    Article • Colloids and Surfaces B Biointerfaces, December 2015, Elsevier

    Marco D'Abramo

  46. The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain

    Article • Oncogene, October 2015, Springer Science + Business Media

    Marco D'Abramo

  47. Theoretical calculation of the pyrene emission properties in different solvents

    Article • Chemical Physics Letters, October 2015, Elsevier

    Marco D'Abramo

  48. Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold

    Article • Journal of Biological Chemistry, June 2015, American Society for Biochemistry & Molecular Biology (ASBMB)

    Marco D'Abramo

  49. Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins

    Article • PLoS ONE, March 2015, PLOS

    Marco D'Abramo

  50. In silico characterization of protein partial molecular volumes and hydration shells

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Marco D'Abramo

  51. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

    Article • Frontiers in Genetics, May 2014, Frontiers

    Marco D'Abramo

  52. Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions

    Article • The Journal of Chemical Physics, April 2014, American Institute of Physics

    Marco D'Abramo

  53. Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution

    Article • Physical Chemistry Chemical Physics, January 2014, Royal Society of Chemistry

    Marco D'Abramo

  54. Molecular mechanisms of activation in CDK2

    Article • Journal of Biomolecular Structure and Dynamics, October 2013, Taylor & Francis

    Marco D'Abramo

  55. Molecular dynamics of the full-length p53 monomer

    Article • Cell Cycle, September 2013, Taylor & Francis

    Marco D'Abramo

  56. On the Nature of DNA Hyperchromic Effect

    Article • The Journal of Physical Chemistry B, July 2013, American Chemical Society (ACS)

    Marco D'Abramo

  57. Non-specific protein–DNA interactions control I-CreI target binding and cleavage

    Article • Nucleic Acids Research, April 2012, Oxford University Press (OUP)

    Marco D'Abramo

  58. Conformational Selection versus Induced Fit in Kinases: The Case of PI3K-γ

    Article • Angewandte Chemie International Edition, December 2011, Wiley

    Marco D'Abramo

  59. Effects of local electric fields on the redox free energy of single stranded DNA

    Article • Chemical Communications, January 2011, Royal Society of Chemistry

    Marco D'Abramo

  60. Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin

    Article • Journal of Chemical Theory and Computation, December 2010, American Chemical Society (ACS)

    Marco D'Abramo

  61. MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

    Article • Structure, November 2010, Elsevier

    Professor Josep Ll. Gelpi, Dr Alberto Perez, Marco D'Abramo

  62. Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

    Article • Journal of Molecular Biology, October 2010, Elsevier

    Marco D'Abramo

  63. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

    Article • Nucleic Acids Research, September 2010, Oxford University Press (OUP)

    Marco D'Abramo

  64. Kinetics of Carbon Monoxide Migration and Binding in Solvated Myoglobin as Revealed by Molecular Dynamics Simulations and Quantum Mechanical Calculations

    Article • The Journal of Physical Chemistry B, December 2009, American Chemical Society (ACS)

    Marco D'Abramo

  65. On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes

    Article • Journal of Chemical Theory and Computation, November 2009, American Chemical Society (ACS)

    Marco D'Abramo

  66. Theoretical Characterization of the Dynamical Behavior and Transport Properties of α,γ-Peptide Nanotubes in Solution

    Article • Journal of the American Chemical Society, November 2009, American Chemical Society (ACS)

    Marco D'Abramo

  67. FlexServ: an integrated tool for the analysis of protein flexibility

    Article • Bioinformatics, May 2009, Oxford University Press (OUP)

    Marco D'Abramo

  68. Theoretical characterization of electronic states in interacting chemical systems

    Article • The Journal of Chemical Physics, February 2009, American Institute of Physics

    Marco D'Abramo

  69. Charge transfer equilibria of aqueous single stranded DNA

    Article • Physical Chemistry Chemical Physics, January 2009, Royal Society of Chemistry

    Marco D'Abramo

  70. What can we learn by comparing experimental and theoretical-computational X-ray scattering data?

    Article • Journal of Molecular Liquids, January 2009, Elsevier

    Marco D'Abramo

  71. Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions With Microwave Fields: The Case Study of Myoglobin

    Article • IEEE Transactions on Microwave Theory and Techniques, November 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Marco D'Abramo

  72. Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data

    Article • The Journal of Chemical Physics, January 2008, American Institute of Physics

    Marco D'Abramo

  73. Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state

    Article • Theoretical Chemistry Accounts, January 2008, Springer Science + Business Media

    Marco D'Abramo

  74. Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water

    Article • Journal of Molecular Structure THEOCHEM, June 2007, Elsevier

    Marco D'Abramo

  75. Theoretical study of intramolecular charge transfer in π-conjugated oligomers

    Article • Chemical Physics Letters, February 2007, Elsevier

    Marco D'Abramo

  76. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin

    Article • Theoretical Chemistry Accounts, January 2007, Springer Science + Business Media

    Marco D'Abramo

  77. On the importance of configurational sampling in theoretical calculation of electronic properties of complex molecular systems: Acetone in water

    Article • Chemical Physics Letters, June 2006, Elsevier

    Marco D'Abramo

  78. Conformational behavior of temporin A and temporin L in aqueous solution: A computational/experimental study

    Article • Biopolymers, February 2006, Wiley

    Marco D'Abramo

  79. Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution

    Article • Physical Chemistry Chemical Physics, January 2006, Royal Society of Chemistry

    Marco D'Abramo

  80. Myoglobin as a Case Study for Molecular Simulations in the Presence of a Microwave Electromagnetic Field

    Article • January 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Marco D'Abramo

  81. Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde

    Article • Journal of Physical Organic Chemistry, January 2006, Wiley

    Marco D'Abramo

  82. Theoretical Characterization of α-Helix and β-Hairpin Folding Kinetics

    Article • Journal of the American Chemical Society, October 2005, American Chemical Society (ACS)

    Marco D'Abramo

  83. Ground and excited electronic state thermodynamics of aqueous carbon monoxide: A theoretical study

    Article • The Journal of Chemical Physics, March 2005, American Institute of Physics

    Marco D'Abramo

  84. Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case

    Article • The Journal of Chemical Physics, March 2005, American Institute of Physics

    Marco D'Abramo

  85. Characterization of liquid behaviour by means of local density fluctuations

    Article • Journal of Molecular Liquids, March 2005, Elsevier

    Marco D'Abramo, Danilo Roccatano

  86. Calculation of the optical rotatory dispersion of solvated alanine by means of the perturbed matrix method

    Article • Chemical Physics Letters, February 2005, Elsevier

    Marco D'Abramo

  87. Theoretical Characterisation of the Electronic Excitation in Liquid Water

    Article • ChemPhysChem, January 2005, Wiley

    Marco D'Abramo

  88. Theoretical Study of the Thermodynamics of a Solvated Peptide: Contryphan Vn

    Article • Physica Scripta, January 2005, Institute of Physics Publishing

    Marco D'Abramo

  89. On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions

    Article • The Journal of Chemical Physics, March 2004, American Institute of Physics

    Marco D'Abramo

  90. Electronic properties of formaldehyde in water: a theoretical study

    Article • Chemical Physics Letters, November 2003, Elsevier

    Marco D'Abramo

  91. Statistical Mechanics and Thermodynamics of Simulated Ionic Solutions

    Article • The Journal of Physical Chemistry B, November 2002, American Chemical Society (ACS)

    Marco D'Abramo